Two institutions provide multilateral venues for countries to discuss food safety measures at the international level: the Codex Alimentarius Commission (Codex) and the World Trade Organization. Both institutions encourage their members to base food safety standards on scientific evidence. In this paper we provide a description of how food safety related scientific evidence is generated and how it is used in the context of risk assessment for international standard-setting at CODEX and in WTO trade disputes. In particular, we discuss the processes leading to policy conclusions on the basis of scientific evidence, with a focus on the interactions involved between private and public sector actors and those between “scientific experts” and others. We identify weaknesses in the current institutional set-up and provide suggestions on how to improve the interaction between different players at the national and international level so as to strengthen the existing system and increase its cost efficiency.